biogems.info - gems for bioinformatics

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#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	1.5.1	13 months	306	12	156345	0	8
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	3.4.2	8 weeks	24	3	83831	0	6
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.5.1	11 months	26	8	60768	0	0
4	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	3 years	15	12	55209	0	0
5	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.11	3 months	117	48	51173	0	2
6	bio gadget		Shintaro Katayama	0.5.0	8 months		1	41268	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.4	5 weeks	16	1	38124	0	28
8	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	2 years	8	1	34837	0	0
9	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	3 years	14	5	32747	0	0
10	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	6 years	17	5	30893	0	0
11	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	5 years	10	36	27825	0	0
12	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	5 years	7	2	26307	0	0
13	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	2 years	13	1	25669	0	0
14	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	0.7.3	2 years	3	2	24903	4	7
15	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	4 years	5	...	24624	0	0
16	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	5 years	1	...	24338	0	0
17	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	2 years	13	3	21882	0	0
18	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	5 years	4	2	21286	0	0
19	obo parser	Ruby parsering for obo files	Matt Yoder	0.4.2	6 years	5	...	21198	0	9
20	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	3 years	10	21	17973	0	0
21	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	4 years	16	3	17848	0	0
22	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.1.0	1 week	11	5	17662	0	8
23	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	5 years	10	...	16866	0	0
24	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	4 years			14146	0	0
25	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	21 months	42	9	14124	0	0
26	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	3 years	11	1	13704	0	0
27	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	5 years	2	1	13301	0	0
28	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	3 years	3	...	13175	0	0
29	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.1.12	17 months			12946	0	0
30	scaffolder	Build genome output files	Michael Barton	0.5.0	4 years	7	...	12795	0	0
31	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	5 years	29	15	12765	0	0
32	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	6 years	1	...	12725	0	0
33	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.4	6 months	2	...	12383	0	0
34	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	4 years	4	...	12363	0	0
35	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	4 years	11	2	12175	0	0
36	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	6 years	1	...	11650	0	0
37	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	5 years	2	...	11483	0	0
38	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	6 years	4	...	11362	0	0
39	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	4 years	7	1	11115	0	0
40	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.9.1	11 months	2	...	10987	0	0
41	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	5 years	3	...	10869	0	0
42	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	5 years	8	2	10780	0	0
43	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	2 years		...	10481	0	0
44	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	2 years		...	10442	0	0
45	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.6.12	17 months	1	...	10333	0	0
46	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	3 years		...	10137	0	1
47	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	5 years	3	...	9669	0	0
48	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	6 years	4	...	9539	0	0
49	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	4 years	2	1	9526	0	2
50	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	9 years	22	1	9514	0	0
51	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	6 years	1	...	8713	0	0
52	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	4 years			8339	0	0
53	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	4 years	5	1	8161	0	0
54	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	6 years	4	...	8072	0	0
55	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	6 years	1	...	7797	0	0
56	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	2 years			7688	0	0
57	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	4 years	2	...	7595	0	0
58	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	6 years	12	...	7497	0	0
59	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	18 months	1	...	7410	0	0
60	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	6 years	40	5	7061	0	0
61	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	14 months		1	6995	0	0
62	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	4 years	2	...	6927	0	0
63	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	5 years	13	19	6860	0	0
64	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	4 years			6794	0	0
65	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	5 years	1	1	6752	0	0
66	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	3 years	4	16	6727	0	0
67	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	5 years	2	...	6676	0	0
68	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.7	7 weeks	16	4	6658	0	53
69	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	22 months	1	...	6542	0	0
70	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.4.0	9 weeks		...	6416	0	7
71	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	5 years	4	1	6242	0	0
72	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	5 years	2	1	6225	0	0
73	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	6 years	1	...	6044	0	0
74	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.1.1	4 months		1	5897	0	0
75	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	4 years			5894	0	0
76	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	4 years		...	5800	0	0
77	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	3 years	1	...	5645	0	0
78	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.5.4	13 months	1	...	5571	0	0
79	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	6 years	1	...	5382	0	0
80	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	5 years	1	...	5202	0	0
81	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	5 years	2	...	5186	0	0
82	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	4 years	2	1	5186	0	0
83	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	5 years	1	...	4766	0	0
84	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	4 years	2	...	4619	0	0
85	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	3 years			4288	0	0
86	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	2 years	2	1	4072	0	0
87	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	8 years	5	...	4038	0	0
88	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.6	5 months	5	2	3988	0	0
89	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	2 years	2	1	3859	0	0
90	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	22 months	3	...	3825	0	0
91	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	4 years	1	...	3682	0	0
92	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	4 years	2	...	3635	0	0
93	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.2.1	3 years	6	...	3528	0	0
94	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	4 years			3495	0	0
95	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	8 years	90	1	3351	0	0
96	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	3 years		...	3301	0	0
97	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	3 years		...	3222	0	0
98	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	6 years	4	...	3202	0	0
99	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	6 years	3	...	3184	0	0
100	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	2 years		...	3168	0	0
101	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	6 years		1	3129	0	0
102	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	3 years	4	...	3095	0	0
103	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.1.0	9 months	3	...	3071	0	0
104	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	7 years	1	...	3060	0	0
105	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	3 years		...	3001	0	0
106	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	6 years	1	...	2955	0	0
107	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	6 years	1	...	2901	0	0
108	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	6 years	2	...	2894	0	0
109	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	5 years	4	...	2866	0	0
110	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	6 years		...	2852	0	0
111	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	5 years	1	...	2852	0	0
112	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	5 years	4	...	2817	0	0
113	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	5 years	1	...	2799	0	0
114	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	6 years	1	...	2798	0	0
115	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	5 years	1	...	2788	0	0
116	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	5 years	3	1	2786	0	0
117	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	5 years	1	...	2764	0	0
118	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	5 years			2642	0	0
119	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	16 months		...	2449	0	0
120	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	4 years		...	2344	0	0
121	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	4 years	2	...	2165	0	0
122	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	2 years		...	2151	0	0
123	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	2 years			2093	0	0
124	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	4 years		...	2077	0	0
125	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	3 years	1	...	1871	0	0
126	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	3 years	1	...	1700	0	0
127	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	3 years	1	...	1605	0	0
128	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	3 years			1568	0	0
129	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	3 years		...	1531	0	0
130	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	3 years		...	1505	0	5
131	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	2 years		...	1469	0	0
132	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	2 years			1379	0	0
133	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	2 years			1322	0	0
134	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	8 years			1317	0	0
135	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	2 years			1099	0	0
136	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	2 years		...	1099	0	0
137	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	2 years	1	...	1072	0	0
138	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	20 months		...	913	0	0
139	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	20 months		...	857	0	0
140	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	16 months		...	620	0	0
141	bio gemma wrapper	Cache gemma with loco	Pjotr Prins	0.92.2	6 weeks		...	401	0	24
142	bio shell	BioRuby shell: interactive analysis environment for BioRuby	BioRuby project	0.0.0	4 weeks		...	189	0	6
143	bio executables	BioRuby executables: utilities bundled with BioRuby	BioRuby project	0.0.0	4 weeks		...	188	0	2
144	bio primer3	pre		pre			...	0	0	0

*) gem downloads (total & last 90 days) from rubygems.org as of 2017-10-18
**) number of commits on GitHub (last 7 days & last 90 days)